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java.lang.ObjectTurboReg_
public class TurboReg_
This class is the only one that is accessed directly by imageJ;
it launches a modeless dialog and dies. Note that it implements
PlugIn rather than PlugInFilter.
| Field Summary | |
|---|---|
private double[][] |
sourcePoints
|
private double[][] |
targetPoints
|
private ij.ImagePlus |
transformedImage
|
| Constructor Summary | |
|---|---|
TurboReg_()
|
|
| Method Summary | |
|---|---|
private ij.ImagePlus |
alignImages(ij.ImagePlus source,
int[] sourceCrop,
ij.ImagePlus target,
int[] targetCrop,
int transformation,
boolean interactive)
|
private ij.ImagePlus[] |
createAdmissibleImageList()
|
private void |
dumpSyntax(java.lang.String options)
|
private java.lang.Boolean |
getInteractive(java.lang.String token)
|
private int |
getPyramidDepth(int sw,
int sh,
int tw,
int th)
|
double[][] |
getSourcePoints()
Accessor method for the (double[][])sourcePoints variable. |
double[][] |
getTargetPoints()
Accessor method for the (double[][])targetPoints variable. |
private java.lang.String[] |
getTokens(java.lang.String options)
|
private int |
getTransformation(java.lang.String token)
|
ij.ImagePlus |
getTransformedImage()
Accessor method for the (ImagePlus)transformedImage
variable. |
void |
run(java.lang.String commandLine)
This method is the only one called by ImageJ. |
private ij.ImagePlus |
transformImage(ij.ImagePlus source,
int width,
int height,
int transformation,
boolean interactive)
|
| Methods inherited from class java.lang.Object |
|---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
|---|
private double[][] sourcePoints
private double[][] targetPoints
private ij.ImagePlus transformedImage
| Constructor Detail |
|---|
public TurboReg_()
| Method Detail |
|---|
public double[][] getSourcePoints()
(double[][])sourcePoints variable.
This variable is valid only after a call to run with the
option -align has been issued. What is returned is a
two-dimensional array of type double[][] that contains
coordinates from the image sourceFilename. These coordinates
are given relative to the original image, before that the cropping
described by the sourceCropLeft, sourceCropTop,
sourceCropRight, and sourceCropBottom has been
applied. These coordinates match those available from
targetPoints. The total number of coordinates, equal to
sourcePoints[*].length, is given by the constant
turboRegPointHandler.NUM_POINTS which corresponds to four
coordinates in the present version. The second index gives the horizontal
component for [0] and the vertical component for
[1]. The number of useful coordinates depends on the
specific transformation for which the alignment has been performed:
translation (1), scaled rotation (2), rotation (3), affine transformation
(3), and bilinear transformation (4).
run(java.lang.String),
getTargetPoints()public double[][] getTargetPoints()
(double[][])targetPoints variable.
This variable is valid only after a call to run with the
option -align has been issued. What is returned is a
two-dimensional array of type double[][] that contains
coordinates from the image targetFilename. These coordinates
are given relative to the original image, before that the cropping
described by the targetCropLeft, targetCropTop,
targetCropRight, and targetCropBottom has been
applied. These coordinates match those available from
sourcePoints. The total number of coordinates, equal to
targetPoints[*].length, is given by the constant
turboRegPointHandler.NUM_POINTS which corresponds to four
coordinates in the present version. The second index gives the horizontal
component for [0] and the vertical component for
[1]. The number of useful coordinates depends on the
specific transformation for which the alignment has been performed:
translation (1), scaled rotation (2), rotation (3), affine transformation
(3), and bilinear transformation (4).
run(java.lang.String),
getSourcePoints()public ij.ImagePlus getTransformedImage()
(ImagePlus)transformedImage
variable. This variable is valid only after a call to run
with the option -transform has been issued. What is returned
is an ImagePlus object of the size described by the
outputWidth and outputHeight parameters of
the call to the run method of TurboReg_.
run(java.lang.String)public void run(java.lang.String commandLine)
| command | parameter | index | comment |
|---|---|---|---|
| −help | 00 | prints out the syntax | |
| −align | 00 | do refine the landmarks | |
| −file −window |
01 | reference type | |
| sourceFilename sourceWindowTitle | 02 | string with optional quotes | |
| sourceCropLeft | 03 | integer | |
| sourceCropTop | 04 | integer | |
| sourceCropRight | 05 | integer | |
| sourceCropBottom | 06 | integer | |
| −file −window | 07 | reference type | |
| targetFilename targetWindowTitle | 08 | string with optional quotes | |
| targetCropLeft | 09 | integer | |
| targetCropTop | 10 | integer | |
| targetCropRight | 11 | integer | |
| targetCropBottom | 12 | integer | |
| −translation −rigidBody −scaledRotation −affine −bilinear |
13 | transformation (TRSAB) | |
| sourcePoints[0][0] | 14 | floating-point (TRSAB) | |
| sourcePoints[0][1] | 15 | floating-point (TRSAB) | |
| targetPoints[0][0] | 16 | floating-point (TRSAB) | |
| targetPoints[0][1] | 17 | floating-point (TRSAB) | |
| sourcePoints[1][0] | 18 | floating-point (RSAB) | |
| sourcePoints[1][1] | 19 | floating-point (RSAB) | |
| targetPoints[1][0] | 20 | floating-point (RSAB) | |
| targetPoints[1][1] | 21 | floating-point (RSAB) | |
| sourcePoints[2][0] | 22 | floating-point (RAB) | |
| sourcePoints[2][1] | 23 | floating-point (RAB) | |
| targetPoints[2][0] | 24 | floating-point (RAB) | |
| targetPoints[2][1] | 25 | floating-point (RAB) | |
| sourcePoints[3][0] | 26 | floating-point (B) | |
| sourcePoints[3][1] | 27 | floating-point (B) | |
| targetPoints[3][0] | 28 | floating-point (B) | |
| targetPoints[3][1] | 29 | floating-point (B) | |
| −hideOutput −showOutput | 18 (T) 22 (S) 26 (RA) 30 (B) | ||
| −transform | 00 | do not refine the landmarks | |
| −file −window | 01 | reference type | |
| sourceFilename sourceWindowTitle | 02 | string with optional quotes | |
| outputWidth | 03 | integer | |
| outputHeight | 04 | integer | |
| −translation −rigidBody −scaledRotation −affine −bilinear | 05 | transformation (TRSAB) | |
| sourcePoints[0][0] | 06 | floating-point (TRSAB) | |
| sourcePoints[0][1] | 07 | floating-point (TRSAB) | |
| targetPoints[0][0] | 08 | floating-point (TRSAB) | |
| targetPoints[0][1] | 09 | floating-point (TRSAB) | |
| sourcePoints[1][0] | 10 | floating-point (RSAB) | |
| sourcePoints[1][1] | 11 | floating-point (RSAB) | |
| targetPoints[1][0] | 12 | floating-point (RSAB) | |
| targetPoints[1][1] | 13 | floating-point (RSAB) | |
| sourcePoints[2][0] | 14 | floating-point (RAB) | |
| sourcePoints[2][1] | 15 | floating-point (RAB) | |
| targetPoints[2][0] | 16 | floating-point (RAB) | |
| targetPoints[2][1] | 17 | floating-point (RAB) | |
| sourcePoints[3][0] | 18 | floating-point (B) | |
| sourcePoints[3][1] | 19 | floating-point (B) | |
| targetPoints[3][0] | 20 | floating-point (B) | |
| targetPoints[3][1] | 21 | floating-point (B) | |
| −hideOutput −showOutput | 10 (T) 14 (S) 18 (RA) 22 (B) |
−align −file path/source.tif 40 80 639 479
−file path/target.tif 0 0 639 479
−translation 320 240 331.7 210 −showOutput
"my path/my file". Escape characters (e.g., a
backslash) are not interpreted.
run in interface ij.plugin.PlugIncommandLine - String optional list of parameters.
private ij.ImagePlus alignImages(ij.ImagePlus source,
int[] sourceCrop,
ij.ImagePlus target,
int[] targetCrop,
int transformation,
boolean interactive)
private ij.ImagePlus[] createAdmissibleImageList()
private void dumpSyntax(java.lang.String options)
private java.lang.Boolean getInteractive(java.lang.String token)
private int getPyramidDepth(int sw,
int sh,
int tw,
int th)
private java.lang.String[] getTokens(java.lang.String options)
private int getTransformation(java.lang.String token)
private ij.ImagePlus transformImage(ij.ImagePlus source,
int width,
int height,
int transformation,
boolean interactive)
|
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